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MB Sample ID: SA018832
| Local Sample ID: | 110705bwasa24_1 |
| Subject ID: | SU000417 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 45-74 |
| Gender: | M/F |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000417 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 45-74 |
| Gender: | M/F |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 110705bwasa24_1 | SA018832 | FL005129 | 65-69 | Age Group |
| 110705bwasa24_1 | SA018832 | FL005129 | Female | Sex |
| 110705bwasa24_1 | SA018832 | FL005129 | Former | Smoking Status |
| 110705bwasa24_1 | SA018832 | FL005129 | - | Diagnosis |
Collection:
| Collection ID: | CO000411 |
| Collection Summary: | In total, 208 patients with lung cancer were selected from 222 patients with non–small-cell lung cancer (NSCLC) with serum available in the CARET repository from blood draws that occurred up to 12 months before diagnosis. Fourteen patients with insufficient sample available for the study were excluded.Two control individuals who were free of lung cancer were matched to each patient case on age at baseline (5-year groups), sex, baseline smoking status (current v former), and study enrollment phase (pilot [1985 to 1988] or full-scale trial [1989 to 1994], thus accounting for sample storage time). For one patient, only a single control could be matched, resulting in a total of 208 patients and 415 controls included in the study. The samples were divided into two sets; samples from 100 matched sets were used for biomarker discovery (the discovery set), and the remaining 108 matched sets were reserved for validation of markers identified by the discovery efforts (the validation set). All CARET participants provided informed consent at recruitment and throughout follow-up, and the institutional review boards at each of the six study centers approved all study procedures. |
| Collection Protocol Filename: | JCO-2015-Wikoff-3880-6.pdf |
| Sample Type: | Blood |
| Blood Serum Or Plasma: | Plasma |
Treatment:
| Treatment ID: | TR000431 |
| Treatment Summary: | Potential confounders and effect modifiers on the DAS and lung cancer association were examined by the Mann-Whitney U test or Kruskal-Wallis test, stratified by case-control status, to assess association between DAS and several potential confounders, including sex, age, fasting time (hours since last meal), body mass index, smoking status (current v former), pack-years, and CARET exposure population (asbestos-exposed v heavy smoker cohort), as well as histology, stage of disease, and time of blood draw with respect to diagnosis (0 to 6 months v 6 to 12 months prior) among patients with lung cancer only. |
| Treatment Protocol Filename: | JCO-2015-Wikoff-3880-6.pdf |
| Human Fasting: | 0-30 Hours |
Sample Preparation:
| Sampleprep ID: | SP000424 |
| Sampleprep Summary: | 1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30μl of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450μL portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450μL aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 μL 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_blood-GCTOF-11082012.pdf |
Combined analysis:
| Analysis ID | AN000633 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC Ion Trap |
| MS instrument name | Varian 210-MS GC Ion Trap |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000458 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Corporation Rtx-5Sil MS |
| Column Pressure: | 7.7 PSI |
| Column Temperature: | 50-330C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50 C ramped to 250 C by 12 C/s |
| Sample Injection: | 0.5 uL |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000566 |
| Analysis ID: | AN000633 |
| Instrument Name: | Varian 210-MS GC Ion Trap |
| Instrument Type: | GC Ion Trap |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250 C |
| Ionization Energy: | 70 eV |
| Mass Accuracy: | Nominal |
| Source Temperature: | 250 C |
| Scan Range Moverz: | 85-500 Da |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 85-500 Da |
| Skimmer Voltage: | 1850 V |
